load Brgo.v3.0anno.Atgoslim.BP.list
load(file.path("..","Annotation_copy","output","v3.0annotation","Brgo.v3.0anno.Atgoslim.BP.list.Rdata"))
load GO.ORA function
GOseq function for Brassica rapa (v3.0)
# GOseq
library(ShortRead);library(goseq);library(GO.db);library("annotate")
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## dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
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## order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
## rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
## union, unique, unsplit, which, which.max, which.min
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## Welcome to Bioconductor
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## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
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## select
## Loading required package: XML
# for ggplot heatmap
## uncompress gz file
system(paste("gunzip -c ",file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.gz")," > ",file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.fa")))
## read cDNA fasta file
Bra.v3.0_cdna<-readDNAStringSet(file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.fa")) # copied from /Volumes/data_work/Data8/NGS_related/Brassica_rapa_Upendra/G3
Bra.v3.0_cdna
## A DNAStringSet instance of length 46250
## width seq names
## [1] 1254 ATGCGACCACCGGGTGTTGTT...GAGTCTCTCTTGCTCGCTTAA BraA01g000010.3C
## [2] 1668 ATGCCAGCAATGCATGCCGTT...AGATGGATCACAAAAGATTAA BraA01g000020.3C
## [3] 957 ATGATGCTTCTCGTTCATACC...AACTTGGAGTTCCCTGAGTGA BraA01g000030.3C
## [4] 1299 ATGAGTCGTCTTCTCCTTGCT...GGGTCACGAGATGAGCTATAA BraA01g000040.3C
## [5] 774 ATGGATTCTGGGCTTCAGCAT...GGAAAGCAGTTCCTTTCGTGA BraA01g000050.3C
## ... ... ...
## [46246] 162 ATGCGTCCGTCCTCAGCTCCC...TCTTTGGTGGTCCGGTTCTAA BraAnng001840.3C
## [46247] 1455 ATGTCTAATCAAGGATCAGGA...ACAGGTTTGTTTAGGTGCTAA BraAnng001850.3C
## [46248] 1011 ATGGACAACGTAATTCTGAAA...TCAGGGAAGAAAAGCCCCTGA BraAnng006150.3C
## [46249] 870 ATGTTTCCAAGACGTACAAGG...AGCAGTTGTCCTTATAGTTAG BraAnng000040.3C
## [46250] 1338 ATGCCGCAACAATACTGGAAC...GGAGAGAACCTTATCTCCTGA BraAnng003440.3C
## remove fasta file
system(paste("rm ",file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.fa"),sep=""))
# GOseq function
GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA<-function(genelist,padjust=0.05,ontology="BP",custom.category.list=Brgo.v3.0anno.Atgoslim.BP.list,Br_cdna=Bra.v3.0_cdna) { # return GO enrichment table, padjus, padjust=0.05.
bias<-nchar(Br_cdna)
names(bias)<-names(Br_cdna)
TF<-(names(bias) %in% genelist)*1
names(TF)<-names(bias)
#print(TF)
pwf<-nullp(TF,bias.data=bias)
#print(pwf$DEgenes)
GO.pval <- goseq(pwf,gene2cat=custom.category.list,use_genes_without_cat=TRUE) # format became different in new goseq version (021111). Does not work (042716)
#GO.pval <- goseq(pwf,gene2cat=Brgo.DF3,use_genes_without_cat=TRUE) # format became different in new goseq version (021111)
#head(GO.pval)
if(ontology=="BP") {
GO.pval2<-subset(GO.pval,ontology=="BP")
} else if(ontology=="CC") {
GO.pval2<-subset(GO.pval,ontology=="CC")
} else {
GO.pval2<-subset(GO.pval,ontology=="MF")
}
GO.pval2$over_represented_padjust<-p.adjust(GO.pval2$over_represented_pvalue,method="BH")
if(GO.pval2$over_represented_padjust[1]>padjust) return("no enriched GO")
else {
enriched.GO<-GO.pval2[GO.pval2$over_represented_padjust<padjust,]
print("enriched.GO is")
print(enriched.GO)
## write Term and Definition
for(i in 1:dim(enriched.GO)[1]) {
if(is.null(Term(GOTERM[enriched.GO[i,"category"]]))) {next} else {
enriched.GO$Term[i]<-Term(GOTERM[[enriched.GO[i,"category"]]])
enriched.GO$Definition[i]<-Definition(GOTERM[[enriched.GO[i,"category"]]])
}
}
return(enriched.GO)
}
}
#
head(Bra.v3.0_cdna)
## A DNAStringSet instance of length 6
## width seq names
## [1] 1254 ATGCGACCACCGGGTGTTGTTTC...CTGAGTCTCTCTTGCTCGCTTAA BraA01g000010.3C
## [2] 1668 ATGCCAGCAATGCATGCCGTTTT...GTAGATGGATCACAAAAGATTAA BraA01g000020.3C
## [3] 957 ATGATGCTTCTCGTTCATACCCG...GGAACTTGGAGTTCCCTGAGTGA BraA01g000030.3C
## [4] 1299 ATGAGTCGTCTTCTCCTTGCTCA...GTGGGTCACGAGATGAGCTATAA BraA01g000040.3C
## [5] 774 ATGGATTCTGGGCTTCAGCATCT...AAGGAAAGCAGTTCCTTTCGTGA BraA01g000050.3C
## [6] 3327 ATGGCGTCCACTCCTCCTCAAAA...GCGGTGGGTTTCAATTTCCTTGA BraA01g000060.3C
# length(bias) # 44239 > 45019 where the bias come from?
# bias.data vector must have the same length as DEgenes vector!
ORA: two afternoon and expression pattern
twoafternoon.trtlive.DEGs.all.v3.0anno<-read_csv(file=file.path("..","output","twoafternoon.trtlive.DEGs.all.v3.0anno.csv"))
## Parsed with column specification:
## cols(
## genes = col_character(),
## logFC = col_double(),
## logCPM = col_double(),
## LR = col_double(),
## PValue = col_double(),
## FDR = col_double(),
## AGI = col_character(),
## At_symbol = col_character(),
## At_short_description = col_character(),
## perc_ID = col_double()
## )
library(dplyr)
#genelist.up<-base::get(paste("../output/",DEG.objs.v3.0annotation.unique[n],sep="")) %>% rownames_to_column() %>% dplyr::filter(logFC>0) # does not work
temp<-twoafternoon.trtlive.DEGs.all.v3.0anno
genelist.up<-temp[temp[,3]>0&temp[,"FDR"]<0.05,"genes"];genelist.down<-temp[temp[,3]<0&temp[,"FDR"]<0.05,"genes"]
print(paste("number of up genes is ",dim(genelist.up)[1]))
## [1] "number of up genes is 1416"
# expression pattern of upregulated genes
gene.of.interest.FDR.up <- twoafternoon.trtlive.DEGs.all.v3.0anno %>% filter(FDR< 0.05,logFC>0) %>%
dplyr::select(genes,logFC,FDR) %>% arrange(FDR)
print("logFC>0")
## [1] "logFC>0"
p.up1<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[1,]);p.up1
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.up2<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[2,]);p.up2
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.up3<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[3,]);p.up3
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.up4<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[4,]);p.up4
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.up5<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[5,]);p.up5
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
# expression pattern of diwbregulated genes
gene.of.interest.FDR.down <- twoafternoon.trtlive.DEGs.all.v3.0anno %>% filter(FDR< 0.05,logFC<0) %>% dplyr::select(genes,logFC,FDR) %>% arrange(FDR)
print("logFC<0")
## [1] "logFC<0"
p.down1<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[1,]);p.down1
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.down2<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[2,]);p.down2
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.down3<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[3,]);p.down3
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.down4<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[4,]);p.down4
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
p.down5<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[5,]);p.down5
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector
#genelist.down<-read_csv(paste("../output/",file,sep="")) %>% dplyr::filter(logFC.genotypeR500<0)
if(dim(genelist.up)[1]<3) {print("Number of up genes is smaller than three. Skip this."); GO.ORA.temp.up<-"no enriched GO";next} else {GO.ORA.temp.up<-GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA(as_vector(genelist.up)) }
## Warning in pcls(G): initial point very close to some inequality constraints
## Using manually entered categories.
## Calculating the p-values...
## 'select()' returned 1:1 mapping between keys and columns
## [1] "enriched.GO is"
## category over_represented_pvalue under_represented_pvalue numDEInCat
## 1210 GO:0010200 1.357094e-12 1.0000000 36
## 2253 GO:0042742 1.061509e-10 1.0000000 61
## 890 GO:0009611 9.615647e-09 1.0000000 39
## 2750 GO:0050832 2.163094e-08 1.0000000 39
## 899 GO:0009626 3.350053e-08 1.0000000 21
## 638 GO:0006952 7.956456e-08 1.0000000 75
## 853 GO:0009407 7.000843e-07 0.9999999 11
## 900 GO:0009627 9.893457e-07 0.9999998 15
## 1174 GO:0010120 2.987504e-06 0.9999998 8
## 894 GO:0009617 3.027497e-06 0.9999991 24
## 557 GO:0006749 4.127199e-06 0.9999994 12
## 646 GO:0006979 4.499773e-06 0.9999982 36
## 3708 GO:2000022 5.272435e-06 0.9999991 13
## 1166 GO:0010112 5.493947e-06 0.9999996 7
## 423 GO:0006468 6.010503e-06 0.9999967 91
## 2859 GO:0051707 1.635476e-05 0.9999968 13
## 972 GO:0009751 1.886256e-05 0.9999932 27
## 1038 GO:0009871 1.984908e-05 0.9999993 5
## 3442 GO:1900067 4.006062e-05 1.0000000 3
## 1107 GO:0010030 4.605592e-05 0.9999934 9
## 855 GO:0009409 5.161047e-05 0.9999755 42
## 3164 GO:0071732 5.481625e-05 0.9999920 9
## 898 GO:0009625 6.533906e-05 0.9999874 11
## 1858 GO:0031348 9.920065e-05 0.9999821 10
## 3114 GO:0071369 1.327728e-04 0.9999777 9
## 607 GO:0006869 1.391666e-04 0.9999608 15
## 2986 GO:0062034 1.434714e-04 0.9999954 4
## 1183 GO:0010150 1.702460e-04 0.9999427 19
## 2917 GO:0055114 1.965588e-04 0.9998735 96
## 49 GO:0000272 2.534934e-04 0.9999663 7
## 921 GO:0009651 2.650096e-04 0.9998502 56
## 2439 GO:0045332 2.706706e-04 0.9999723 6
## 478 GO:0006562 2.881153e-04 0.9999969 3
## 185 GO:0002229 3.712637e-04 0.9998926 14
## 3094 GO:0071281 4.180861e-04 0.9999083 10
## numInCat
## 1210 286
## 2253 726
## 890 419
## 2750 469
## 899 140
## 638 1165
## 853 67
## 900 104
## 1174 27
## 894 241
## 557 85
## 646 502
## 3708 89
## 1166 22
## 423 1484
## 2859 97
## 972 347
## 1038 11
## 3442 3
## 1107 54
## 855 696
## 3164 52
## 898 84
## 1858 64
## 3114 62
## 607 208
## 2986 8
## 1183 219
## 2917 1923
## 49 39
## 921 1045
## 2439 23
## 478 4
## 185 126
## 3094 77
## term
## 1210 response to chitin
## 2253 defense response to bacterium
## 890 response to wounding
## 2750 defense response to fungus
## 899 plant-type hypersensitive response
## 638 defense response
## 853 toxin catabolic process
## 900 systemic acquired resistance
## 1174 camalexin biosynthetic process
## 894 response to bacterium
## 557 glutathione metabolic process
## 646 response to oxidative stress
## 3708 regulation of jasmonic acid mediated signaling pathway
## 1166 regulation of systemic acquired resistance
## 423 protein phosphorylation
## 2859 response to other organism
## 972 response to salicylic acid
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 3442 regulation of cellular response to alkaline pH
## 1107 positive regulation of seed germination
## 855 response to cold
## 3164 cellular response to nitric oxide
## 898 response to insect
## 1858 negative regulation of defense response
## 3114 cellular response to ethylene stimulus
## 607 lipid transport
## 2986 L-pipecolic acid biosynthetic process
## 1183 leaf senescence
## 2917 oxidation-reduction process
## 49 polysaccharide catabolic process
## 921 response to salt stress
## 2439 phospholipid translocation
## 478 proline catabolic process
## 185 defense response to oomycetes
## 3094 cellular response to iron ion
## ontology over_represented_padjust
## 1210 BP 5.142029e-09
## 2253 BP 2.011029e-07
## 890 BP 1.214456e-05
## 2750 BP 2.048991e-05
## 899 BP 2.538670e-05
## 638 BP 5.024502e-05
## 853 BP 3.789456e-04
## 900 BP 4.685789e-04
## 1174 BP 1.147119e-03
## 894 BP 1.147119e-03
## 557 BP 1.420803e-03
## 646 BP 1.420803e-03
## 3708 BP 1.486897e-03
## 1166 BP 1.486897e-03
## 423 BP 1.518253e-03
## 2859 BP 3.873011e-03
## 972 BP 4.178232e-03
## 1038 BP 4.178232e-03
## 3442 BP 7.988931e-03
## 1107 BP 8.725295e-03
## 855 BP 9.312003e-03
## 3164 BP 9.440854e-03
## 898 BP 1.076390e-02
## 1858 BP 1.566130e-02
## 3114 BP 2.012305e-02
## 607 BP 2.013382e-02
## 2986 BP 2.013382e-02
## 1183 BP 2.303794e-02
## 2917 BP 2.568143e-02
## 49 BP 3.201621e-02
## 921 BP 3.204910e-02
## 2439 BP 3.204910e-02
## 478 BP 3.308087e-02
## 185 BP 4.137407e-02
## 3094 BP 4.526081e-02
print(paste("number of down genes is ",dim(genelist.down)[1]))
## [1] "number of down genes is 58"
if(dim(genelist.down)[1]<3) {print("Number of up genes is smaller than three. Skip this."); GO.ORA.temp.down<-"no enriched GO"; next} else {GO.ORA.temp.down<-GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA(as_vector(genelist.down)) }
## Using manually entered categories.
## Calculating the p-values...
## 'select()' returned 1:1 mapping between keys and columns
# handling "no enriched GO"
# genelist.names<-c("GO.ORA.temp.up_down","GO.ORA.temp.down_up") # test
x<-list(GO.ORA.temp.up=GO.ORA.temp.up,
GO.ORA.temp.down=GO.ORA.temp.down) # list
x<-x[!x=="no enriched GO"] # remove "no enriched GO" result
## add sample info and FC info and save GO.ORA result
if(length(x)==0) {next} else {GO.ORA.result<-x}
GO.ORA.result
## $GO.ORA.temp.up
## category over_represented_pvalue under_represented_pvalue numDEInCat
## 1210 GO:0010200 1.357094e-12 1.0000000 36
## 2253 GO:0042742 1.061509e-10 1.0000000 61
## 890 GO:0009611 9.615647e-09 1.0000000 39
## 2750 GO:0050832 2.163094e-08 1.0000000 39
## 899 GO:0009626 3.350053e-08 1.0000000 21
## 638 GO:0006952 7.956456e-08 1.0000000 75
## 853 GO:0009407 7.000843e-07 0.9999999 11
## 900 GO:0009627 9.893457e-07 0.9999998 15
## 1174 GO:0010120 2.987504e-06 0.9999998 8
## 894 GO:0009617 3.027497e-06 0.9999991 24
## 557 GO:0006749 4.127199e-06 0.9999994 12
## 646 GO:0006979 4.499773e-06 0.9999982 36
## 3708 GO:2000022 5.272435e-06 0.9999991 13
## 1166 GO:0010112 5.493947e-06 0.9999996 7
## 423 GO:0006468 6.010503e-06 0.9999967 91
## 2859 GO:0051707 1.635476e-05 0.9999968 13
## 972 GO:0009751 1.886256e-05 0.9999932 27
## 1038 GO:0009871 1.984908e-05 0.9999993 5
## 3442 GO:1900067 4.006062e-05 1.0000000 3
## 1107 GO:0010030 4.605592e-05 0.9999934 9
## 855 GO:0009409 5.161047e-05 0.9999755 42
## 3164 GO:0071732 5.481625e-05 0.9999920 9
## 898 GO:0009625 6.533906e-05 0.9999874 11
## 1858 GO:0031348 9.920065e-05 0.9999821 10
## 3114 GO:0071369 1.327728e-04 0.9999777 9
## 607 GO:0006869 1.391666e-04 0.9999608 15
## 2986 GO:0062034 1.434714e-04 0.9999954 4
## 1183 GO:0010150 1.702460e-04 0.9999427 19
## 2917 GO:0055114 1.965588e-04 0.9998735 96
## 49 GO:0000272 2.534934e-04 0.9999663 7
## 921 GO:0009651 2.650096e-04 0.9998502 56
## 2439 GO:0045332 2.706706e-04 0.9999723 6
## 478 GO:0006562 2.881153e-04 0.9999969 3
## 185 GO:0002229 3.712637e-04 0.9998926 14
## 3094 GO:0071281 4.180861e-04 0.9999083 10
## numInCat
## 1210 286
## 2253 726
## 890 419
## 2750 469
## 899 140
## 638 1165
## 853 67
## 900 104
## 1174 27
## 894 241
## 557 85
## 646 502
## 3708 89
## 1166 22
## 423 1484
## 2859 97
## 972 347
## 1038 11
## 3442 3
## 1107 54
## 855 696
## 3164 52
## 898 84
## 1858 64
## 3114 62
## 607 208
## 2986 8
## 1183 219
## 2917 1923
## 49 39
## 921 1045
## 2439 23
## 478 4
## 185 126
## 3094 77
## term
## 1210 response to chitin
## 2253 defense response to bacterium
## 890 response to wounding
## 2750 defense response to fungus
## 899 plant-type hypersensitive response
## 638 defense response
## 853 toxin catabolic process
## 900 systemic acquired resistance
## 1174 camalexin biosynthetic process
## 894 response to bacterium
## 557 glutathione metabolic process
## 646 response to oxidative stress
## 3708 regulation of jasmonic acid mediated signaling pathway
## 1166 regulation of systemic acquired resistance
## 423 protein phosphorylation
## 2859 response to other organism
## 972 response to salicylic acid
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 3442 regulation of cellular response to alkaline pH
## 1107 positive regulation of seed germination
## 855 response to cold
## 3164 cellular response to nitric oxide
## 898 response to insect
## 1858 negative regulation of defense response
## 3114 cellular response to ethylene stimulus
## 607 lipid transport
## 2986 L-pipecolic acid biosynthetic process
## 1183 leaf senescence
## 2917 oxidation-reduction process
## 49 polysaccharide catabolic process
## 921 response to salt stress
## 2439 phospholipid translocation
## 478 proline catabolic process
## 185 defense response to oomycetes
## 3094 cellular response to iron ion
## ontology over_represented_padjust
## 1210 BP 5.142029e-09
## 2253 BP 2.011029e-07
## 890 BP 1.214456e-05
## 2750 BP 2.048991e-05
## 899 BP 2.538670e-05
## 638 BP 5.024502e-05
## 853 BP 3.789456e-04
## 900 BP 4.685789e-04
## 1174 BP 1.147119e-03
## 894 BP 1.147119e-03
## 557 BP 1.420803e-03
## 646 BP 1.420803e-03
## 3708 BP 1.486897e-03
## 1166 BP 1.486897e-03
## 423 BP 1.518253e-03
## 2859 BP 3.873011e-03
## 972 BP 4.178232e-03
## 1038 BP 4.178232e-03
## 3442 BP 7.988931e-03
## 1107 BP 8.725295e-03
## 855 BP 9.312003e-03
## 3164 BP 9.440854e-03
## 898 BP 1.076390e-02
## 1858 BP 1.566130e-02
## 3114 BP 2.012305e-02
## 607 BP 2.013382e-02
## 2986 BP 2.013382e-02
## 1183 BP 2.303794e-02
## 2917 BP 2.568143e-02
## 49 BP 3.201621e-02
## 921 BP 3.204910e-02
## 2439 BP 3.204910e-02
## 478 BP 3.308087e-02
## 185 BP 4.137407e-02
## 3094 BP 4.526081e-02
## Term
## 1210 response to chitin
## 2253 defense response to bacterium
## 890 response to wounding
## 2750 defense response to fungus
## 899 plant-type hypersensitive response
## 638 defense response
## 853 toxin catabolic process
## 900 systemic acquired resistance
## 1174 camalexin biosynthetic process
## 894 response to bacterium
## 557 glutathione metabolic process
## 646 response to oxidative stress
## 3708 regulation of jasmonic acid mediated signaling pathway
## 1166 regulation of systemic acquired resistance
## 423 protein phosphorylation
## 2859 response to other organism
## 972 response to salicylic acid
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 3442 regulation of cellular response to alkaline pH
## 1107 positive regulation of seed germination
## 855 response to cold
## 3164 cellular response to nitric oxide
## 898 response to insect
## 1858 negative regulation of defense response
## 3114 cellular response to ethylene stimulus
## 607 lipid transport
## 2986 L-pipecolic acid biosynthetic process
## 1183 leaf senescence
## 2917 oxidation-reduction process
## 49 polysaccharide catabolic process
## 921 response to salt stress
## 2439 phospholipid translocation
## 478 proline catabolic process
## 185 defense response to oomycetes
## 3094 cellular response to iron ion
## Definition
## 1210 A process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chitin stimulus.
## 2253 Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
## 890 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
## 2750 Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
## 899 The rapid, localized death of plant cells in response to invasion by a pathogen.
## 638 Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
## 853 The chemical reactions and pathways resulting in the breakdown of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
## 900 The salicylic acid mediated response to a pathogen which confers broad spectrum resistance.
## 1174 The chemical reactions and pathways resulting in the formation of camalexin, an indole phytoalexin.
## 894 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
## 557 The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
## 646 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
## 3708 Any process that modulates the frequency, rate or extent of jasmonic acid mediated signaling pathway.
## 1166 Any process that modulates the frequency, rate or extent of systemic acquired resistance.
## 423 The process of introducing a phosphate group on to a protein.
## 2859 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism.
## 972 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a salicylic acid stimulus.
## 1038 The series of molecular signals mediated by ethylene (ethene) involved in jasmonic acid/ethylene dependent systemic resistance.
## 3442 <NA>
## 1107 Any process that activates or increase the rate of seed germination.
## 855 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
## 3164 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.
## 898 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from an insect.
## 1858 Any process that stops, prevents, or reduces the frequency, rate or extent of a defense response.
## 3114 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethylene (ethene) stimulus.
## 607 The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
## 2986 The chemical reactions and pathways resulting in the formation of L-pipecolic acid, a metabolite of lysine.
## 1183 The process that occurs in a leaf near the end of its active life that is associated with the dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism.
## 2917 A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
## 49 The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
## 921 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
## 2439 The movement of a phospholipid molecule from one leaflet of a membrane bilayer to the opposite leaflet.
## 478 The chemical reactions and pathways resulting in the breakdown of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
## 185 Reactions triggered in response to the presence of oomycetes that act to protect the cell or organism.
## 3094 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus.
# save data
save(GO.ORA.result,file="../output/GOseq.timecourse.twoafternoon.Brgo.v3.0.Atgoslim.BP.list.enrich.Rdata")
session info
sessionInfo
## function (package = NULL)
## {
## z <- list()
## z$R.version <- R.Version()
## z$platform <- z$R.version$platform
## if (nzchar(.Platform$r_arch))
## z$platform <- paste(z$platform, .Platform$r_arch, sep = "/")
## z$platform <- paste0(z$platform, " (", 8 * .Machine$sizeof.pointer,
## "-bit)")
## z$locale <- Sys.getlocale()
## z$running <- osVersion
## z$RNGkind <- RNGkind()
## if (is.null(package)) {
## package <- grep("^package:", search(), value = TRUE)
## keep <- vapply(package, function(x) x == "package:base" ||
## !is.null(attr(as.environment(x), "path")), NA)
## package <- .rmpkg(package[keep])
## }
## pkgDesc <- lapply(package, packageDescription, encoding = NA)
## if (length(package) == 0)
## stop("no valid packages were specified")
## basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) &&
## x$Priority == "base")
## z$basePkgs <- package[basePkgs]
## if (any(!basePkgs)) {
## z$otherPkgs <- pkgDesc[!basePkgs]
## names(z$otherPkgs) <- package[!basePkgs]
## }
## loadedOnly <- loadedNamespaces()
## loadedOnly <- loadedOnly[!(loadedOnly %in% package)]
## if (length(loadedOnly)) {
## names(loadedOnly) <- loadedOnly
## pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription))
## z$loadedOnly <- pkgDesc[loadedOnly]
## }
## z$matprod <- as.character(options("matprod"))
## es <- extSoftVersion()
## z$BLAS <- as.character(es["BLAS"])
## z$LAPACK <- La_library()
## class(z) <- "sessionInfo"
## z
## }
## <bytecode: 0x7fcf2d6aee40>
## <environment: namespace:utils>